Matthew,
Thanks I can try your second suggestion. Looks easier.
Roman Osman
Icahn School of Medicine at Mount Sinai
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From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Sent: Sunday, April 23, 2023 2:15:28 PM
To: Osman, Roman <roman.osman.mssm.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: {SPAM?} [AMBER] Separating a trajectory by output from clusterdihedral
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Hi Roman,
The onlyframes option to trajout takes a range of frames. Maybe you can specify multiple ranges separated by commas. But I imagine it may be difficult to construct comma-separated ranges from the output you have.
Another option may be to use a script to write a cpptraj intput file with 25,000 lines like the following:
trajin <name_of_traj> <frame #> <frame #> 1
In other words, load in each frame for a given cluster separately, and then save all the loaded frames for that cluster to a new (pseudo) trajectory. Repeat for the second cluster. I’ve used this strategy before, but not for so many frames; you may encounter a memory issue.
I hope these suggestions help.
Best,
Matthew
From: Osman, Roman via AMBER <amber.ambermd.org>
Date: Sunday, April 23, 2023 at 1:39 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: {SPAM?} [AMBER] Separating a trajectory by output from clusterdihedral
*Message sent from a system outside of UConn.*
Hello,
I would like to separate a trajectory by the clusters produced by clusterdihedral.
I have two dihedrals that cluster into two clusters with nearly equal populations because their changes are correlated.
In the out file from cpptraj I get a list of frames that belong to each cluster, but because the trajectory has 50000 snapshots the list is quite long (~25,000 entries).
The question is whether I can use this list to write the trajectory with onlyframes and supply this long list.
Or perhaps is another way to cluster the trajectory by the dihedrals and write the two clusters separately.
Thanks for your help.
Roman Osman
Professor
Department of Pharmacological Sciences
Icahn School of Medicine at Mount Sinai
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Received on Sun Apr 23 2023 - 12:00:02 PDT
